Author: Pensoft Editorial Team

Extensive practical guide to DNA-based biodiversity assessment methods published as a ‘living’ document by DNAqua-Net COST Action

Between 2016 and 2021, over 500 researchers collaborated within the DNAqua-Net international network, funded by the European Union’s European Cooperation in Science and Technology programme (COST), with the goal to develop and advance biodiversity assessment methods based on analysis of DNA obtained from the environment (e.g. river water) or from unsorted collections of organisms. 

Such innovative methods are a real game changer when it comes to large-scale assessment of biodiversity and ecological monitoring, as collecting environmental samples that are sent to the lab for analysis is much cheaper, faster and non-invasive, compared with capturing and examining live organisms. However, large-scale adoption has been hindered by a lack of standardisation and official guidance. 

Recognising the urgent need to scale up ecological monitoring as we respond to the biodiversity and climate crises, the DNAqua-Net team published a guidance document for the implementation of DNA-based biomonitoring tools.

The guide considers four different types of samples: water, sediments, invertebrate collections and diatoms, and two primary analysis types: single species detection via qPCR and similar targeted methods; and assessment of biological communities via DNA metabarcoding. At each stage of the field and laboratory process the guide sets out the scientific consensus, as well as the choices that need to be made and the trade-offs they entail. In particular, the guide considers how the choices may be influenced by common practical constraints such as logistics, time and budget. Available in an Advanced Book format, the guidelines will be updated as the technology continues to evolve.

Leaders of DNAqua-Net are Prof. Dr. Florian Leese of the University of Duisburg-Essen (Germany) and Dr. Agnès Bouchez of the French National Institute for Agriculture, Food, and Environment (INRAE). The core writing team for the present guide book involves Dr. Micaela Hellström (MIX Research AB, Sweden), Dr. Kat Bruce (NatureMetrics Ltd., UK), Dr. Rosetta Blackman (University of Zurich and EAWAG, Switzerland), Dr. Sarah Bourlat (LIB/Museum Koenig, Germany), and Prof. Kristy Deiner (ETH Zurich and SimplexDNA AG, Switzerland).

“Back in 2016 we realised that all around the globe researchers are testing new eDNA methods, developing individual solutions and products. While this is excellent, we need to reach a consensus and provide this consensus to stakeholders from the applied sectors”, 

says Florian Leese.
This video was created as part of EU COST Action DNAqua-Net (CA15219) and shows how environmental DNA (eDNA) can be sampled and analysed from aquatic ecosystems. It shows the whole cycle from the start to final results. 
Credit: DNAqua-Net

The guide’s lead author Dr. Kat Bruce adds:

“The urgency of addressing the twin biodiversity and climate crises means that we need to accelerate the adoption of new technologies that can provide data and insights at large scales. In doing so, we walk a tricky line to agree on sufficiently standardised methods that can be usefully applied as soon as they add value, while still continuing to develop them further and innovate within the field. It was a daunting task to seek consensus from several hundred scientists working in a fast-moving field, but we found that our technology is based on a strong foundation of knowledge and there was a high level of agreement on the core principles – even if the details vary and different users make different choices depending on their environmental, financial or logistical constraints.”

Looking back on the last four years that culminated in the publication of a “living” research publication, Prof. Dr. Kristy Deiner says:

“The document took many twists and turns through more than ten versions and passionate discussions across many workshops and late night drinks. All in the days when we could linger at conferences without fear of the pandemic weighing on us. As we worked to find consensus, one thing was clear: we had a lot to say and a standard review paper was not going to cut it. With the knowledge and experience gathered across the DNAqua-Net, it made sense to not limit this flow of information, but rather to try and tackle it head on and use it to address the many questions we’ve all struggled with while developing DNA-based biodiversity survey methods.”

Now that the document – or at least its first version – is publicly available, the researchers are already planning for the next steps and challenges.

“The bottom line is we’ve come a long way in the last ten years. We have a buffet of methods for which many produce accurate, reliable and actionable data to the aid of biodiversity monitoring and conservation. While there is still much work to be done, the many unanswered questions are because the uptake is so broad. With this broad uptake comes novel challenges, but also new insights and a diversity of minds with new ideas to address them. As said this is planned to be a living document and we welcome continued inputs no matter how great or small,” says Deiner.

Dr. Micaela Hellström recalls:

“The book evolved over the four years of COST Action DNAqua-Net which made it possible for the many scientists and stakeholders involved to collaborate and exchange knowledge on an unprecedented scale. Our whole team is well aware of the urgent need to monitor biodiversity loss and to provide accurate species distribution information on large scales, to protect the species that are left. This was a strong driving force for all of us involved in the production of this document. We need consensus on how to coherently collect biodiversity data to fully understand changes in nature.”

“It was a great and intense experience to be a part of the five-person core writing team. In the months prior to submitting the document, we spent countless hours, weekends and late nights researching the field, communicating with researchers and stakeholders, and joining vivid Zoom discussions. As a result, the present book provides solid guidance on multiple eDNA monitoring methods that are – or will soon become – available as the field moves forward.” 

***

The DNAqua-Net team invites fellow researchers and practitioners to provide their feedback and personal contributions using the contacts below.

***

Original source:

Bruce K, Blackman R, Bourlat SJ, Hellström AM, Bakker J, Bista I, Bohmann K, Bouchez A, Brys R, Clark K, Elbrecht V, Fazi S, Fonseca V, Hänfling B, Leese F, Mächler E, Mahon AR, Meissner K, Panksep K, Pawlowski J, Schmidt Yáñez P, Seymour M, Thalinger B, Valentini A, Woodcock P, Traugott M, Vasselon V, Deiner K (2021) A practical guide to DNA-based methods for biodiversity assessment. Advanced Books. https://doi.org/10.3897/ab.e68634

Accidental tree wound reveals novel symbiotic behavior

Despite significant movement restrictions during the first wave of the pandemic in Panama City, a group of curious high school students roamed their neighborhood drilling holes into Cecropia trees and documenting how Azteca alfari ants responded to damage to their host plant.

During the pandemic, five curious high school students accidentally discovered how Azteca alfari ants respond to damage to their Cecropia host trees. Photo by Donna Conlon

One afternoon, during the early days of the COVID-19 pandemic in Panama, a bored teenager with a slingshot and a clay ball accidentally shot entry and exit holes in a Cecropia tree trunk. These are “ant-plant” trees, which famously cooperate with fierce Azteca ants; the trees provide shelter and food to the ants, and in exchange the ants defend their leaves against herbivores. The next morning, to his surprise, the Azteca alfari ants living within the Cecropia trunk had patched up the wound.

This unexpected occurrence drove five curious high school students, with time on their hands, to participate in the Smithsonian Tropical Research Institute’s (STRI) volunteer program, and they enlisted STRI scientist William T. Wcislo’s help in devising their experiment. Despite significant movement restrictions during the first wave of the pandemic, they roamed their neighborhood drilling holes into Cecropia trees and documenting the ants’ responses to the damage.

They found that as soon as the plants had holes drilled into them, the ants ran to the wound area and began patching it up. Within 2.5 hours, the size of the hole had been significantly reduced and it was often completely repaired within 24 hours.

Although some Azteca ants are known to defend their Cecropia host plants against herbivores, these new results, published in the Journal of Hymenoptera Research, reveal that not only do the ants behave in ways to minimize damage to their hosts, but when damage does occur, they actively work to fix it, particularly when their brood is directly threatened.

“I was totally surprised by the results,” says William Wcislo. “And I was impressed by how they developed a simple way to test the idea that ants repair damage to their home.” 

Azteca ant and Cecropia plant responses to wounds in the stems a a sealed hole after 24 hours, but not yet filled in to the stem surface (arrow) b a fully patched and filled-in hole after 24 hrs, oozing sap from the ant-sealed wound (arrow) c a natural plant scar surrounding a 6.4 mm hole that was fully sealed by the ants, approximately 5 months later d a hole in a plant without ants after 24 hrs, showing the green wall of the opposite side of the stem (arrow).

Sloths and silky anteaters often visit Cecropia trees and their sharp toenails sometimes pierce the wood, so the researchers speculate that these occurrences, which are far more common and ancient threats to the Cecropia than teenagers shooting clay balls at them, could have led Azteca alfari ants to evolve the observed repair behavior when their host plant is damaged. 

Their experiment also left them with new questions, since not all of the ant colonies repaired the damage to their host plants. Understanding what factors influence the ants to take action could be the subject of future research for these budding scientists, although perhaps to be addressed after graduating from high school.

“Sometimes messing around with a slingshot has a good outcome,” said lead author Alex Wcislo. “This project allowed us to experience first-hand all the intricacies behind a scientific study. All in all, it was a great learning experience, especially considering the difficulties associated with fulfilling this due to COVID-19.”

Research article:

Wcislo A, Graham X, Stevens S, Toppe JE, Wcislo L, Wcislo WT (2021) Azteca ants repair damage to their Cecropia host plants. Journal of Hymenoptera Research 88: 61-70. https://doi.org/10.3897/jhr.88.75855

The tallest begonia species in all Asia found in Tibet, China

Chinese researchers have discovered the tallest Begonia recorded in Asia. The plant belongs to a new species aptly called Begonia giganticaulis.

With over 2050 known species, Begonia is one of the largest plant genera. Since most begonias are small weeds, a begonia taller than a human is a very unusual sight. However, the newly discovered Begonia giganticaulis is one of the few exceptions.

Flowers of Begonia giganticaulis.

In 2019, Dr. Daike Tian and his colleagues initiated a field survey on wild begonias in Tibet, China. On September 10, 2020, when Dr. Tian saw a huge begonia in full bloom during surveys in the county of Mêdog, he got instantly excited. After checking its flowers, he was confident it represented a new species.

  • Dr. Daike Tian with an individual of Begonia giganticaulis. Photo by Qing-Gong Mao
  • The research team measures the height of a Begonia giganticaulis individual at its collection site. Photo by Qing-Gong Mao

From a small population with a few dozens of individuals, Dr. Tian collected two of the tallest ones to measure them and prepare specimens necessary for further study. One of them was 3.6 meters tall, the thickest part of its ground stem close to 12 cm in diameter. To measure it correctly, he had to ask the driver to stand on top of the vehicle. In order to carry them back to Shanghai and prepare dry specimens, Dr. Tian had to cut each plant into four sections.

A Begonia giganticaulis plant is cut up for easier transportation
A Begonia giganticaulis plant is cut up for easier transportation. Photo by Daike Tian

To date, this plant is the tallest begonia recorded in the whole of Asia.

Begonia giganticaulis, recently described as a new species in the peer-reviewed journal PhytoKeys, grows on slopes under forests along streams at elevation of 450–1400 m. It is fragmentally distributed in southern Tibet, which was one of the reasons that its conservation status was assigned to Endangered according to the IUCN Red List Categories and Criteria.

The research team pose with a specimen of Begonia giganticaulis at the first Chinese begonia show in Shanghai Chenshan Botanical Garden.
The research team pose with a specimen of Begonia giganticaulis at the first Chinese begonia show in Shanghai Chenshan Botanical Garden. Photo by Meiqin Zhu

After being dried at a herbarium and mounted on a large board, the dried specimen was measured at 3.1 m tall and 2.5 m wide. To our knowledge, this is the world’s largest specimen of a Begonia species. In October 2020, the visitors who saw it at the first Chinese begonia show in Shanghai Chenshan Botanical Garden were shocked by its huge size.

Currently, the staff of Chenshan Herbarium is applying for Guinness World Records for this specimen.

Research article:

Tian D-K, Wang W-G, Dong L-N, Xiao Y, Zheng M-M, Ge B-J (2021) A new species (Begonia giganticaulis) of Begoniaceae from southern Xizang (Tibet) of China. PhytoKeys 187: 189-205.https://doi.org/10.3897/phytokeys.187.75854

A year of biodiversity: Top 10 new species of 2021 from Pensoft journals, Part 2

While 2021 may have been a stressful and, frankly, strange year, in the world of biodiversity there has been plenty to celebrate! Out of the many new species we published in our journals this year, we’ve curated a selection of the 10 most spectacular discoveries. The world hides amazing creatures just waiting to be found – and we’re making this happen, one new species at a time.

Read Part 1 of the Top 10 new species of 2021 here.

5. The Instagram model

Many students and young researchers are encouraged to explore biodiversity by starting from their own backyard. Yes, but how often do they find undescribed snake species in there?

This is exactly what happened to Virendar K. Bhardwaj, a master student in Guru Nanak Dev University in Amritsar. Confined to his home in Chamba, India because of the COVID-19 lockdown, he started photographing any wildlife he came across and uploading it on his Instagram account. One of his images showed a beautiful kukri snake.

The picture immediately caught the attention of Zeeshan A. Mirza (National Centre for Biological Sciences, Bangalore) and Harshil Patel (Veer Narmad South Gujarat University, Surat), who worked together with Virendar to describe it as a new species under the name Oligodon churahensis.

“It is quite interesting to see how an image on Instagram led to the discovery of such a pretty snake that, until very recently, remained hidden to the world,” Zeeshan A. Mirza told us earlier this month.

“What’s even more interesting is that the exploration of your own backyard may yield still undocumented species. Lately, people have been eager to travel to remote biodiversity hotspots to find new or rare species, but if one looks in their own backyard, they may end up finding a new species right there.”

Published in: Evolutionary Systematics

4. The tiny snail with an athletic name

Do freshwater snails make good tennis players? Well, one of them certainly has the name for it.

Enter Travunijana djokovici, a new species of aquatic snail named after famous Serbian ten­nis player Novak Djokovic.

Found in a karstic spring near Podgorica, the capital of Montenegro, T. Djokovici is part of the family of mud snails, which inhabit fresh or brackish water, including caves and subterranean habitats.

The tiny snail was discovered by Slovak biospeleologist Jozef Grego and Montenegrin zoologist Vladimir Pešić of the University of Montenegro, who claim they named it after the renowned tennis player “to acknowledge his inspiring enthusiasm and energy.”.

To discover some of the world’s rarest animals that inhabit the unique underground habitats of the Dinaric karst, to reach inaccessible cave and spring habitats and for the restless work during processing of the collected material, you need Novak’s energy and enthusiasm,” they add.

Amazingly, Novak Djokovic found out that he’s now a namesake to a tiny snail, and he even had a comment.

“I am honoured that a new species of snail was named after me because I am a big fan of nature and ecosystems and I appreciate all kinds of animals and plants,” he says in an Eurosport article. “I don’t know how symbolic this is, because throughout my career I always tried to be fast and then a snail was named after me,” he joked. “Maybe it’s a message for me, telling me to slow down a bit!”

Published in: Subterranean Biology

3. The Coronavirus caddisfly

The COVID-19 pandemic has undoubtedly affected all of us, and the scientific world is no exception. Fieldwork got postponed, museums remained closed, arranging meet-ups and travel became almost impossible.

Scientists used this as a drive and inspiration as they continued their hard work on new discoveries. Only this year, we published the descriptions of the beetle Trigonopterus corona, the wasp Allorhogas quarentenus, and, yes, the caddisfly Potamophylax coronavirus.

P. coronavirus was collected near a stream in the Bjeshkët e Nemuna National Park in Kosovo by a team of scientists led by Professor Halil Ibrahimi of the University of Prishtina. After molecular and morphological analyses, it was described as a caddisfly species new to science. Its name will be an eternal memory of an extremely difficult period.

In a broader sense, the researchers also wish to bring attention to “another silent pandemic occurring on freshwater organisms in Kosovo’s rivers,” caused by the pollution and degradation of freshwater habitats, as well as the activity increasing in recent years of mismanaged hydropower plants. Particularly, the river basin of the Lumbardhi i Deçanit River, where the new species was discovered, has turned into a ‘battlefield’ for scientists and civil society on one side and the management of the hydropower plant operating on this river on the other.

P. coronavirus is part of the small insect order of Trichoptera, which is very sensitive to water pollution and habitat deterioration. The authors of the species argue that it is a small-scale endemic taxon, very sensitive to the ongoing activities in Lumbardhi i Deçanit river, and failure to understand this may drive it, along with many other species, towards extinction.

Published in: Biodiversity Data Journal

2. The cutest peacock spider ever

If you think spiders can’t be cute, you’ve probably never seen a peacock spider. They have big forward-facing eyes, and their males perform fun courtship dances.

Citizen scientist Sheryl Holliday was the first to spot this vibrant spider while walking in Mount Gambier, Australia, and she posted her find on Facebook. It was later described as a new species by arachnologist Joseph Schubert of Museums Victoria.

Coloured bright orange, it was called Maratus Nemo, after the popular Disney character.

‘It has a really vibrant orange face with white stripes on it, which kind of looks like a clown fish, so I thought Nemo would be a really suitable name for it,’ Joseph Schubert says.

Maratus Nemo is probably the first influencer arachnid – his curious story, bright colours and fun name practically made him an internet star overnight.

Published in: Evolutionary Systematics

1. The tiny ant that challenges gender stereotypes

Found in Ecuador’s evergreen tropical forests, this miniature trap jaw ant bears the curious Latin name Strumigenys ayersthey. Unlike most species named in honour of people, whose names end with -ae (after females) and –i (after males), S. ayersthey might be the only species in the world to have a scientific name with the suffix –they.

“In contrast to the traditional naming practices that identify individuals as one of two distinct genders, we have chosen a non-Latinized portmanteau honoring the artist Jeremy Ayers and representing people that do not identify with conventional binary gender assignments, Strumigenys ayersthey,” authors Philipp Hoenle of the Technical University of
Darmstadt and Douglas Booher of Yale University state in their paper.

“Strumigenys ayersthey sp. nov. is thus inclusively named in honor of Jeremy Ayers for the multitude of humans among the spectrum of gender who have been unrepresented under traditional naming practices.”

Curiously, it was no other than lead singer and lyricist of the American alternative rock band R.E.M. Michael Stipe that joined Booher in writing the etymology section for the research article, where they explain the origin of the species name and honor their mutual friend, activist and artist Jeremy Ayers.

This ant can be distinguished by its predominantly smooth and shining cuticle surface and long trap-jaw mandibles, which make it unique among nearly a thousand species of its genus.

“Such a beautiful and rare animal was just the species to celebrate both biological and human diversity,” Douglas Booher said.

Published in: ZooKeys

Scientists discover White-handed gibbons that have been evolving in the south of Malaysia

Genetic assessment of captive gibbons to identify their species and subspecies is an important step before any conservation actions. A group of wildlife researchers recently discovered a previously unknown population of white-handed gibbons (subspecies lar) from Peninsular Malaysia. Their findings are now published in the open-access journal ZooKeys. Betsy and Lola are among the captive white-handed gibbons undergoing a strict rehabilitation process before being released back to the wild.

Many captive gibbons kept in zoos and rescue centres have been seized from illegal pet trade, private collectors, and plantations where their natural habitats are getting destroyed. 

In 2013, the National Wildlife Rescue Centre (NWRC) of the Department of Wildlife and National Parks (PERHILITAN) was established in Peninsular Malaysia to help with the rehabilitation of wildlife species – including gibbons – before they are reintroduced or translocated back to the wild. Under the Primate Rehabilitation Programme initiated by PERHILITAN, captive gibbons have to go through a number of procedures and assessments, where their taxonomy and genetics might be examined, before they can go back to living in the wild.

Members of the research team at National Wildlife Forensic Laboratory of DWNP. Photo by PERHILITAN

Following the Guidelines for Reintroductions and Other Conservation Translocations provided by the IUCN Species Survival Commission, researchers Dr Jeffrine J. Rovie-Ryan from Universiti Malaysia Sarawak and Millawati Gani and colleagues from the National Wildlife Forensic Laboratory of PERHILITAN conducted a genetic assessment on 12 captive white-handed gibbons in NWRC. Determining the subspecies and origin of the animals is an important step that informs further decisions on their translocation and reintroduction.

In a research paper published in the open-access journal ZooKeys, the team describes a previously unknown southern population of the white-handed gibbon subspecies lar living in Peninsular Malaysia. In what started as a straightforward species and subspecies identification process using DNA technology, the researchers discovered unusual mutations in the DNA of the studied gibbons. This is how the researchers found themselves before a distinct population, which they concluded must have been evolving in isolation.

Lola (left) and Betsy (right), two of the White-handed gibbons of the Hylobates lar lar subspecies undergoing rehabilitation process at Pulau Ungka, NWRC. Photo by Hani Nabilia and PERHILITAN

“Given the prolonged isolation, it is likely that the southern population has undergone some local speciation, but this finding should be regarded as preliminary and requires further investigation,” explained Dr Jeffrine. Furthermore, the researchers suggest there might be a northern population inhabiting Southern Thailand.

Still going through rehabilitation, the gibbons from the study have been pre-released into a semi-wild enclosure known as Pulau Ungka (Gibbon Island), where their recovery is closely monitored by primate experts of PERHILITAN.

Research article:

Gani M, Rovie-Ryan JJ, Sitam FT, Mohd Kulaimi, NA, Zheng, CC, Atiqah AN, Abd Rahim, NM, Mohammed AA (2021) Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobates lar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programme. ZooKeys 1076: 25–41 (2021), doi: 10.3897/zookeys.1076.73262

A year of biodiversity: Top 10 new species of 2021 from Pensoft journals, Part 1

With 2022 round the corner, we thought we’d start off the celebrations by looking back to some the most memorable discoveries of 2021. And what a year it has been! Many new species made their debuts on the pages of Pensoft journals – here’s our selection of the most exciting animals, plants and fungi that we published in 2021.

With 2022 round the corner, we thought we’d start off the celebrations by looking back to some the most memorable discoveries of 2021. And what a year it has been! Many new species made their debuts on the pages of Pensoft journals – here’s our selection of the most exciting animals, plants and fungi that we published in 2021.

10. The delicious wild oak mushroom

It’s amazing that edible species, long known to local communities, can still present a novelty for science. This was the case with Cantharellus veraecrucis, a chanterelle from – that’s right, Veracruz, Mexico.

During the rainy season, locals harvest this mushroom from tropical oak forests to sell it or enjoy it as a delicacy; this is probably why they’ve dubbed it “Oak mushroom”.

Published in: MycoKeys

9. The master of disguise

If you ever see a leaf insect, there’s a good chance you won’t notice it – these little critters are masters of camouflaging.

This picture was taken in 2014, when Jérôme Constant and Joachim Bresseel from the Royal Belgian Institute of Natural Sciences were enjoying a night walk in Vietnam’s Nui Chua National Park. It wasn’t until this year, though, that this beauty got its own scientific name: Cryptophyllium nuichuaense. Named after the park where it was found, it is one of 13 new species of leaf insects described in our journal ZooKeys this February.

This leaf insect, like many others, is endemic to Vietnam. This is why the researchers who found itcall for the creation of more protected areas in order to keep this precious biodiversity intact.

Published in: ZooKeys

8. The Neil Gaiman spider

Unlike most spiders, trapdoor spiders don’t use silk to make a web. Instead, they live in burrows lined with silk that they cover with a “trapdoor”. They are relatively widely spread, but you’d rarely encounter one out in the open, because they spend most of their lives underground.

This is probably why arachnologists and spider lovers the world over got so excited when Dr. Rebecca Godwin (Piedmont University, GA) and Dr. Jason Bond (University of California, Davis, CA) described 33 new species of trapdoor spiders from the genus Ummidia – in addition to the 27 already known.

Dr. Rebecca Godwin talks to L. Brian Patrick about her discovery of 33 new species of trapdoor spiders on his podcast New Species.

One of the 33 is Ummidia neilgaimani, named after fantasy and horror writer Neil Gaiman. A particular favorite of Dr. Godwin, Gaiman is the author of a number of books with spider-based characters. His novel American Gods features a character based on the West African spider god Anansi and a World Tree “one hour south of Blacksburg,” not far from the type locality of this species. He’s also part of the documentary Sixteen Legs, in his own words “An amazing film about Tasmanian cave spider sex.”

“I think anything we can do to increase people’s interest in the diversity around them is worthwhile and giving species names that people recognize but that still have relevant meaning is one way to do that,” says Dr. Godwin.

Published in: ZooKeys

7. The deadly Chinese-goddess snake

Bungarus suzhenae was only described as a new species this year, but its reputation preceded it – in a bad way. Researchers were already familiar with a notorious black-and-white banded krait that bit herpetologists on expeditions in Myanmar and China – in one infamous case, to death. After extensive morphological and phylogenetical analysis, the researchers were finally able to confirm it as new to science.

The story behind B. suzhenae’s name is interesting, too: it was named after a character from the traditional Chinese myth ‘Legend of White Snake’. The powerful snake goddess Bai Su Zhen is to this day regarded as a symbol of true love and good-heartedness in China. 

Snakebites from kraits – including this one – are known to have a high mortality. This is why the new knowledge on B. suzhenae and its description as a new species are essential to the research on its venom and an important step in the development of antivenom and improved snakebite treatment.

Published in: ZooKeys

6. The ephemeral fairy lanterns

Commonly known as “fairy lanterns”, plants of the genus Thismia are very rare and small in size. They are mycoheterotrophic, which means they live in close association with fungi from which they acquire most of their nutrition. They’re also very elusive, growing in dark, remote rainforests, and visible only when they emerge to flower and set seed after heavy rain.

In fact, researchers were only able to find one specimen of the new T. sitimeriamiae, which they discovered in the Terengganu State of Malaysia – the rest of the population had been destroyed by wild boars.

Just discovered, T. sitimeriamiae may already be threatened by extinction – which is why the research team that discovered it suggest that this exceptionally rare plant is classified as Critically Endangered.

Published in: PhytoKeys

Part 2 coming soon – stay tuned!

Decade-old photographs shared on social media give away a new species of pygmy grasshopper

While scrolling through iNaturalist – a social network where professional and citizen scientists share their photographs, in order to map biodiversity observations from across the globe – a group of students from Croatia discovered a couple of curious pictures, taken in 2008 in the Peruvian rainforest and posted in 2018. What they were looking at was a pygmy grasshopper sporting a unique pattern of lively colors. The motley insect was nothing they have so far encountered in the scientific literature.

While scrolling through iNaturalist – a social network where professional and citizen scientists share their photographs, in order to map biodiversity observations from across the globe – a group of students from Croatia discovered a couple of curious pictures, taken in 2008 in the Peruvian rainforest and posted in 2018. What they were looking at was a pygmy grasshopper sporting a unique pattern of lively colors. The motley insect was nothing they have so far encountered in the scientific literature.

The scientist and photographer Roberto Sindaco, Museo Civico di Storia naturale (Torino, Italy) graciously shared his camera roll with Niko Kasalo, Maks Deranja, and Karmela Adžić, graduate students under the mentorship of Josip Skejo, all currently affiliated with University of Zagreb, Faculty of Science, Croatia. Together, they published a paper describing the yet to be named insect in the open-access scientific journal Journal of Orthoptera Research.

Typically, new species are described from specimens collected from their natural habitats and then deposited in a museum to be preserved for future reference. The authors, possessing several high-quality photographs, decided to challenge the norm and name the new species based on photographs only. The paper was initially rejected, but a compromise was reached—it could be published with the species name removed.

The International Code of Zoological nomenclature is a document that contains regulations for proper scientific naming of animal species. It allows naming species from photographs, but the practice is generally looked down upon. Thus, the authors decided to use the nameless species to draw attention to this problem and bring more clarity. Names in zoology consist of two words: the genus name and the species name. As the species name was denied, the grasshopper is now mysteriously referred to as „the nameless Scaria“.

Another important message of this paper is how citizen science portals, such as iNaturalist, allow everybody interested in nature to contribute to ‘real’ scientific work by posting their findings online.

The authors believe that including laypeople in the scientific process can help bridge the communication gap between scientists and the general population, dissipating the growing suspicion towards science. The researchers urge everybody to engage with nature around them and capture its beauty with their camera lens. 

“Only by interacting with nature can we truly feel how much we might lose if we do not take care of it, and care is urgently needed,”

said the authors of the study.
Male of the nameless Scaria species
Photo by Roberto Sindaco

Original source:

Kasalo N, Deranja M, Adžić K, Sindaco R, Skejo J (2021) Discovering insect species based on photographs only: The case of a nameless species of the genus Scaria (Orthoptera: Tetrigidae). Journal of Orthoptera Research 30(2): 173-184. https://doi.org/10.3897/jor.30.65885

Fossil Record, a Natural History Museum of Berlin journal moves to ARPHA

Having been publishing its historically renowned Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution in partnership with Pensoft since 2014, the Museum extends the collaboration by moving a third signature journal

Having been publishing its historically renowned scientific journals Deutsche Entomologische Zeitschrift (DEZ) and Zoosystematics and Evolution (ZSE) in partnership with the scholarly publisher Pensoft and its ARPHA Platform since 2014, the Natural History Museum of Berlin (Museum für Naturkunde Berlin) now extends the collaboration by moving a third signature journal: Fossil Record. 

Launched in 1998 under the name Mitteilungen aus dem Museum für Naturkunde Berlin, Geowissenschaftliche Reihe, Fossil Record is the Natural History Museum of Berlin’s palaeontological journal. Published in two issues a year, the open-access scientific outlet covers research from all areas of palaeontology, including the taxonomy and systematics of fossil organisms, biostratigraphy, palaeoecology, and evolution. It deals with all taxonomic groups, including invertebrates, microfossils, plants, and vertebrates.

Following its move to ARPHA, Fossil Record is to utilise the whole package of ARPHA Platform’s services, including its fast-track, end-to-end publishing module, designed to appeal to readers, authors, reviewers and editors alike. 

With ARPHA, each submitted manuscript is carried through the review, editing, publication, dissemination and archiving stages without leaving the platform’s collaboration-centred online environment. The articles are made available in PDF and machine-readable JATS XML formats, as well as semantically enriched HTML for better and mobile-friendly reader experience. 

As a result, the journal’s articles are as easy to discover, access, reuse and cite as possible. Once published, the content is indexed and archived instantaneously and its underlying data exported to relevant specialised databases. Simultaneously, a suite of various metrics is enabled to facilitate tracking the usage of articles and sub-article elements, such as figures and tables.

“We have deeply enjoyed our collaboration with the Natural History Museum of Berlin for the past seven years that started with two great journals moving to our scholarly portfolio and advanced open access. Now, I am delighted to strengthen this wonderful partnership by welcoming Fossil Record and its fantastic editorial team to the families of ARPHA and Pensoft. I am certain that together we will not only repeat the success we had with DEZ and ZSE, but will actually build on it,”

says Prof. Dr Lyubomir Penev, founder and CEO at ARPHA and Pensoft.

About the Natural History Museum of Berlin:

The “Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science” is an integrated research museum within the Leibniz Association. It is one of the most important research institutions worldwide in the areas of biological and geological evolution and biodiversity.

The Museum’s mission is to discover and describe life and earth – with people, through dialogue. As an excellent research museum and innovative communication platform, it wants to engage with and influence the scientific and societal discourse about the future of our planet, worldwide. Its vision, strategy and structure make the museum an excellent research museum. The Natural History Museum of Berlin has research partners in Berlin, Germany and approximately 60 other countries. Over 700,000 visitors per year as well as steadily increasing participation in educational and other events show that the Museum has become an innovative communication centre that helps shape the scientific and social dialogue about the future of our earth.

Digitising the Natural History Museum London’s entire collection could contribute over £2 billion to the global economy

In a world first, the Natural History Museum, London, has collaborated with economic consultants, Frontier Economics Ltd, to explore the economic and societal value of digitising natural history collections and concluded that digitisation has the potential to see a seven to tenfold return on investment. Whilst significant progress is already being made at the Museum, additional investment is needed in order to unlock the full potential of the Museum’s vast collections – more than 80 million objects. The project’s report is published in the open science scientific journal Research Ideas and Outcomes (RIO Journal).

One of the Museum’s digitisers imaging a butterfly to join the 4.93 million specimens already available online. 
© The Trustees of the Natural History Museum, London

The societal benefits of digitising natural history collections extends to global advancements in food security, biodiversity conservation, medicine discovery, minerals exploration, and beyond. Brand new, rigorous economic report predicts investing in digitising natural history museum collections could also result in a tenfold return. The Natural History Museum, London, has so far made over 4.9 million digitised specimens available freely online – over 28 billion records have been downloaded over 429,000 download events over the past six years. 

Digitisation at the Natural History Museum, London 

Digitisation is the process of creating and sharing the data associated with Museum specimens. To digitise a specimen, all its related information is added to an online database. This typically includes where and when it was collected and who found it, and can include photographs, scans and other molecular data if available. Natural history collections are a unique record of biodiversity dating back hundreds of years, and geodiversity dating back millennia. Creating and sharing data this way enables science that would have otherwise been impossible, and we accelerate the rate at which important discoveries are made from our collections.  

The Natural History Museum’s collection of 80 million items is one of the largest and most historically and geographically diverse in the world. By unlocking the collection online, the Museum provides free and open access for global researchers, scientists, artists and more. Since 2015, the Museum has made 4.9 million specimens available on the Museum’s Data Portal, which have seen more than 28 billion downloads over 427,000 download events. 

This means the Museum has digitised  about 6% of its collections to date. Because digitisation is expensive, costing tens of millions of pounds, it is difficult to make a case for further investment without better understanding the value of this digitisation and its benefits. 

In 2021, the Museum decided to explore the economic impacts of collections data in more depth, and commissioned Frontier Economics to undertake modelling, resulting in this project report, now made publicly available in the open-science journal Research Ideas and Outcomes (RIO Journal), and confirming benefits in excess of £2 billion over 30 years. While the methods in this report are relevant to collections globally, this modelling focuses on benefits to the UK, and is intended to support the Museum’s own digitisation work, as well as a current scoping study funded by the Arts & Humanities Research Council about the case for digitising all UK natural science collections as a research infrastructure.

“Sharing data from our collections can transform scientific research and help find solutions for nature and from nature. Our digitised collections have helped establish the baseline plant biodiversity in the Amazon, find wheat crops that are more resilient to climate change and support research into potential zoonotic origins of Covid-19. The research that comes from sharing our specimens has immense potential to transform our world and help both people and the planet thrive,“

says Helen Hardy, Science Digital Programme Manager at the Natural History Museum.

How digitisation impacts scientific research?

The data from museum collections accelerates scientific research, which in turn creates benefits for society and the economy across a wide range of sectors. Frontier Economics Ltd have looked at the impact of collections data in five of these sectors: biodiversity conservation, invasive species, medicines discovery, agricultural research and development and mineral exploration. 

“The Natural History Museum’s collection is a real treasure trove which, if made easily accessible to scientists all over the world through digitisation, has the potential to unlock ground-breaking research in any number of areas. Predicting exactly how the data will be used in future is clearly very uncertain. We have looked at the potential value that new research could create in just five areas focussing on a relatively narrow set of outcomes. We find that the value at stake is extremely large, running into billions,”

says Dan Popov, Economist at Frontier Economics Ltd.

The new analyses attempt to estimate the economic value of these benefits using a range of approaches, with the results in broad agreement that the benefits of digitisation are at least ten times greater than the costs. This represents a compelling case for investment in museum digital infrastructure without which the many benefits will not be realised.

“This new analysis shows that the data locked up in our collections has significant societal and economic value, but we need investment to help us release it,“

adds Professor Ken Norris, Head of the Life Sciences Department at the Natural History Museum.

Other benefits could include improvements to the resilience of agricultural crops by better understanding their wild relatives, research into invasive species which can cause significant damage to ecosystems and crops, and improving the accuracy of mining.  

Finally, there are other impacts that such work could have on how science is conducted itself. The very act of digitising specimens means that researchers anywhere on the planet can access these collections, saving time and money that may have been spent as scientists travelled to see specific objects.

The value of research enabled by digitisation of natural history collections can be estimated by looking at specific areas where the Museum’s collections contribute towards scientific research and subsequently impact the wider economy. 
© Frontier Economics Ltd.

Original source: 

Popov D, Roychoudhury P, Hardy H, Livermore L, Norris K (2021) The Value of Digitising Natural History Collections. Research Ideas and Outcomes 7: e78844. https://doi.org/10.3897/rio.7.e78844

Standardised expert system method for Navarre grasslands classification based on diagnostic species

Guest blog post by Itziar García-Mijangos

Grasslands represent some of the largest and most diverse biomes of the world, yet they remain undervalued and under-researched. Extending in all continents except Antarctica, they host thousands of habitat specialist endemic species, support agricultural production, people’s livelihoods based on traditional and indigenous lifestyles, and several other ecosystem services such as pollination and water regulation.

Calamintho acini-Seselietum montani in Munarriz (south of Andia Range)

Palaearctic grasslands represent the richest habitats for vascular plants at small spatial scales but are seriously threatened due to land use change. European grasslands experienced two extreme ends of the land-use gradient, intensification of land use on productive lands and abandonment of marginal lands, and both resulted in the loss of grassland biodiversity. It is necessary to understand their biodiversity patterns and how they relate to land use to be able to design conservation and management actions. This understanding requires the harmonization and standardization of grassland classification that leads to a consistent syntaxonomy at the European level and can increase the usefulness of vegetation typologies for conservation and management.

We provide important insights to grasslands, with special focus on dry grasslands, from the western part of Europe (Navarre region, Spain), which constitutes a new step on the pan-European grassland classification. For this purpose, we used 958 relevés distributed across all the region and grassland types, 119 containing also information on bryophytes and lichens. The data used are available in EVA and GrassPlot databases.

The five phytosociological classes most represented in Navarre are distributed according to elevation, climate, soil and topographic variables. The class Lygeo-Stipetea develops in the most Mediterranean areas. On the other hand, the classes Nardetea and Elyno-Seslerietea develop at the highest elevations, linked to the highest annual precipitation and are distributed in the northern areas. Regarding soil, topographic and structural variables the class Nardetea presents the highest soil depth and is also the most acidophilous one. The class Elyno-Seslerietea is characterised by a higher cover of stones and rocks as well as higher soil organic matter content, and, together with Nardetea and Molinio-Arrhenatheretea, is the poorest in soil carbonate content. Conversely, Lygeo-Stipetea stands out by its high soil carbonate content and low soil organic matter. Molinio-Arrhenatheretea stands out for its high cover of the herb layer and cryptogams.

Lygeum spartum communities in Bardenas Reales

We would like to highlight that bryophytes and lichens, contrary to past assumptions, are core elements of these grasslands and particularly the Mediterranean ones of Lygeo-Stipetea, both in terms of biodiversity and of diagnostic species.

We provide, for the first time, an electronic expert system for grasslands in Navarre, based on diagnostic species of each hierarchical phytosociological level from class to association. This expert system can be implemented in the JUICE program and allows the unanimous assignment of any new relevé by means of its species composition to one of the different categories established, which is of enormous value particularly for practitioners. We provide, also for the first time, a detailed databased characterisation and comparison of the syntaxa in terms of their environmental conditions and biodiversity.

Research article:

García-Mijangos I, Berastegi A, Biurrun I, Dembicz I, Janišová M, Kuzemko A, Vynokurov D, Ambarlı D, Etayo J, Filibeck G, Jandt U, Natcheva R, Yildiz O, Dengler J (2021) Grasslands of Navarre (Spain), focusing on the Festuco–Brometea: classification, hierarchical expert system and characterisation. Vegetation Classification and Survey 2: 195-231. https://doi.org/10.3897/VCS/2021/69614